About Us

The ARC Centre of Excellence in Bioinformatics

The Australian Research Council (ARC) Centre in Bioinformatics was initially funded for the five years 2003-2007. ARC subsequently upgraded our centre to an ARC Centre of Excellence and extended its funding through December 2010. Since January 2011 we have continued under a more-focused mandate, thanks to strategic support of partner institutions.

ACB is headquartered at the Institute for Molecular Bioscience at The University of Queensland.

ACB since 2011:

Our partner institutions are:

Macquarie University (Sydney)
The University of Newcastle (Newcastle)
The University of Queensland (Brisbane)

Our Associates are:

Professor Mark Ragan, Director (The University of Queensland)
Dr Timothy Bailey (The University of Queensland)
Dr Nicholas Hamilton (The University of Queensland)
Professor Pablo Moscato (The University of Newcastle)
Professor Shoba Ranganathan (Macquarie University)

Our mission is to

  • promote bioinformatics, including bioinformatics research, in Australia through workshops,conferences and events, and through academic and professional societies;
  • work with national bodies and others to develop a coordinated approach to advanced training in bioinformatics nationally, and in our partner institutions;
  • organise and host the annual national Winter School in Mathematical and Computational Biology;
  • work within our institutions and nationally to ensure that needs of the bioinformatics community are addressed by national research infrastructure; and promote stronger ties between the Australian bioinformatics community and the International Society for Computational Biology, and with the Association of Asian Societies of Bioinformatics.

 

ACB 2008-2010:

Our partner institutions were:

The Australian National University (Canberra)
Deakin University (Melbourne)
Macquarie University (Sydney)
The University of Newcastle (Newcastle)
The University of Queensland (Brisbane)

We also had three overseas partner institutions:
IBM Thomas J. Watson Research Center (USA)
The University of Auckland (New Zealand)
The University of Tennessee (USA)

ACB is a multi-nodal, interdisciplinary centre that uniquely brings together researchers in genomic and post-genomic bioinformatics, cell and structural biology, mathematics, statistics, computer science, information technology, and systems analysis. Our aim is to produce a deep understanding of how information in the genome is transformed into structure and function in the mammalian cell.

We are committed to:

  • Research excellence providing insights into genome-phenome biology.
  • An advanced education and training program that fosters excellence, exposes students from diverse disciplines to new perspectives in bioinformatics, and generates human capital.
  • Improved access to skills, tools and facilities at the interface among genomic and post-genomic biology, molecular cell biology, mathematics, statistics, and computing and information sciences.
  • Critical mass and a national focus for genome-phenome bioinformatics in Australia.

We aim to:

  • Integrate insights and new developments in mathematics, statistics, computing and information sciences, genomic and post-genomic biology, and molecular cell biology.
  • Mutually enrich biomolecular research, mathematics, computer science and information technology.
  • Apply innovative laboratory-based experimental phenomic biology to illuminate the development and differentiation of the mammalian cell.
  • Play a leading role in the national and international bioinformatics agenda and in the generation of human capital, enhancing critical mass and national focus in bioinformatics and computational biosciences.

Our objectives are to:

  • Examine how the genome comes to life in the mammalian cell during differentiation and development.
  • Use empirical data from advanced microarray, tomographic and sequencing technologies to construct quantitative dynamic models of selected cellular regulatory networks and subcellular systems.
  • Develop advanced algorithmic, statistical and computational methods and knowledge engineering systems, and apply them to extend, refine and inter-relate these models.
  • Deliver advanced prototypes of our integrated data and visual framework for hypothesis-testing, validation discovery, the Visible Cell™, and use them to understand more fundamentally the mammalian cell as an information system.

Our investigators have active research collaborations and linkages with a great many overseas institutions, including:

  • Academic Sinica
  • ETH, Switzerland
  • European Bioinformatics Institute (EBI)
  • Fudan University
  • Harvard University
  • Howard Hughes Research Institute, Janelia Farm
  • Israel Institute of Technology (Technion)
  • Korea Advanced Institute for Science and Technology (KAIST)
  • Max-Planck-Institute for Biochemistry
  • Massachusetts Institute of Technology (MIT)
  • National University of Singapore
  • Oak Ridge National Laboratory
  • Oxford University
  • QosCosGRID Consortium (Europe)
  • RIKEN Genomic Sciences Centre
  • San Diego Supercomputer Center
  • University of California, San Diego
  • University of California, Santa Cruz
  • University of Tokyo
  • US Department of Energy Joint Genome Institute (JGI)
  • Wuhan University

Our research was organised into four Research Programs and 11 Projects:

Program 1: The Visible Cell™: linking genome and phenome
Project 1.1: Generation of subcellular localisation data in mammalian cells.
Project 1.2: Project and data management for Visible Cell™.
Project 1.3:  Data analysis and knowledge discovery in very large biological network databases.

Program 2:  Phenotype-informed discovery of networks and systems.
Project 2.1: Computational discovery of gene-regulatory motifs and motif clusters.
Project 2.2: Differential expression of genes towards pathway discovery.
Project 2.3:  Discovery and modelling of RNA-based regulatory networks.

Program 3:  Modelling dynamic cellular processes.
Project 3.1: Mathematical modelling of genetic regulatory networks and biochemical pathways.
Project 3.2: Modelling and visualising biological processes in complex spatial environments.

Program 4: Algorithms for graphs and networks.
Project 4.1: Elaboration of the Vertex Cover problem.
Project 4.2: Optimisation-based approaches to large systems.
Project 4.3: External-memory algorithms for analysis of massive graphs.

Our core technologies include algorithmics and analysis of computational complexity, statistics, machine learning, pattern discovery, computational modelling and simulation, advanced database architectures, automated discovery pipelines and workflows, specialised mark-up languages and ontologies, semantic web technologies, advanced scientific visualisation, high-throughput array-based genomic technologies, confocal video microscopy and high-resolution electron tomographic imaging of cells.

Investigators and students in ACB have access to advanced array platforms, highly capable instruments for biological microscopy and tomography, shared-memory and array supercomputers, advanced visualisation facilities, petabyte storage, high-bandwidth transmission between geographical nodes, and facilities for online collaboration.

ACB and our host institutions partner with major Australian research centres including:

  • ARC Centre for Complex Systems
  • Australian Centre for Plant Functional Genomics
  • Australian Genome Research Foundation
  • CSIRO Livestock Industry
  • CSIRO Mathematical and Information Sciences
  • CRC for Chronic Inflammatory Disease
  • e-Health Research Centre, CSIRO
  • Hunter Medical Research Institute
  • NCRIS Platforms for Collaboration
  • National ICT Australia (NICTA)
  • Queensland Cyber Infrastructure Foundation
  • Queensland Department of Primary Industries & Fisheries
  • Queensland Facility for Advanced Bioinformatics
  • SRC in Functional and Applied Genomics
  • Westmead Millennium Institute of Health Research

We are well connected into national and international initiatives in e-science and Grid computing. Opportunities exist for postgraduate and other advanced training in all of these areas.

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